After participating in several Civil War campaigns, including the successful final Battle of Cynthiana against John Hunt Morgan, Burbridge in June 1864 was given command over the state of Kentucky to deal with the growing problem of Confederateguerrilla campaigns. This began an extended period of military siege that would last through early 1865, beginning with martial law authorized by PresidentAbraham Lincoln. On July 16, 1864, Burbridge issued Order No. 59 which declared: "Whenever an unarmed Union citizen is murdered, four guerrillas will be selected from the prison and publicly shot to death at the most convenient place near the scene of the outrages."[1] During Burbridge's rule in Kentucky, he directed the execution and imprisonment of numerous people, including public figures, on charges of treason and other high crimes, many of which were baseless.[2]

While continuing in charge of Kentucky, in October 1864, Burbridge led Union assaults against the salt works near the town of Saltville, Virginia as part of the Battle of Saltville. Burbridge controversially led black troops into battle, which ultimately failed. Wounded troops left behind were killed by Confederate soldiers, with special ire directed toward the black troops.

During the 1864 presidential campaign, Burbridge tried to ensure re-election of Lincoln, suppressing support for George B. McClellan. His actions included arresting prominent persons favoring the candidate, including Lieutenant Governor Richard T. Jacob, and Judge Bullitt, both of whom he deported to Richmond, Virginia.

After a falling out with GovernorThomas E. Bramlette, including an attempt to take control of his troops and arms in February 1865, Burbridge was dismissed from his role of overseeing operations in Kentucky. Bramlette had quickly complained by telegram to Secretary of War Stanton, writing:

This unwarranted assumption of power by an imbecile commander is doubtless instigated by those who have long sought to provoke an issue with the State, and which I have prevented.

Lincoln revoked Burbridge's order, and decided to replace the general with Major General John Palmer. Burbridge soon resigned from the army.